+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32050 | ||||||||||||||||||||||||||||||
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Title | Al-bound structure of the AtALMT1 mutant M60A | ||||||||||||||||||||||||||||||
Map data | Al-bound structure of the AtALMT1 mutant M60A | ||||||||||||||||||||||||||||||
Sample |
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Function / homology | malate transmembrane transporter activity / malate transmembrane transport / Aluminum-activated malate transporter / Aluminium activated malate transporter / response to aluminum ion / monoatomic ion transmembrane transport / plasma membrane / Aluminum-activated malate transporter 1 Function and homology information | ||||||||||||||||||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||||||||||||||||||||
Authors | Wang J | ||||||||||||||||||||||||||||||
Funding support | China, 9 items
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Citation | Journal: Cell Res / Year: 2022 Title: Structural basis of ALMT1-mediated aluminum resistance in Arabidopsis. Authors: Jiangqin Wang / Xiafei Yu / Zhong Jie Ding / Xiaokang Zhang / Yanping Luo / Ximing Xu / Yuan Xie / Xiaoxiao Li / Tian Yuan / Shao Jian Zheng / Wei Yang / Jiangtao Guo / Abstract: The plant aluminum (Al)-activated malate transporter ALMT1 mediates the efflux of malate to chelate the Al in acidic soils and underlies the plant Al resistance. Here we present cryo-electron ...The plant aluminum (Al)-activated malate transporter ALMT1 mediates the efflux of malate to chelate the Al in acidic soils and underlies the plant Al resistance. Here we present cryo-electron microscopy (cryo-EM) structures of Arabidopsis thaliana ALMT1 (AtALMT1) in the apo, malate-bound, and Al-bound states at neutral and/or acidic pH at up to 3.0 Å resolution. The AtALMT1 dimer assembles an anion channel and each subunit contains six transmembrane helices (TMs) and six cytosolic α-helices. Two pairs of Arg residues are located in the center of the channel pore and contribute to malate recognition. Al binds at the extracellular side of AtALMT1 and induces conformational changes of the TM1-2 loop and the TM5-6 loop, resulting in the opening of the extracellular gate. These structures, along with electrophysiological measurements, molecular dynamic simulations, and mutagenesis study in Arabidopsis, elucidate the structural basis for Al-activated malate transport by ALMT1. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_32050.map.gz | 19.3 MB | EMDB map data format | |
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Header (meta data) | emd-32050-v30.xml emd-32050.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
Images | emd_32050.png | 21.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32050 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32050 | HTTPS FTP |
-Related structure data
Related structure data | 7vojMC 7vq3C 7vq4C 7vq5C 7vq7C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32050.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Al-bound structure of the AtALMT1 mutant M60A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.014 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Al-bound protein sample of the AtALMT1 mutant M60A
Entire | Name: Al-bound protein sample of the AtALMT1 mutant M60A |
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Components |
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-Supramolecule #1: Al-bound protein sample of the AtALMT1 mutant M60A
Supramolecule | Name: Al-bound protein sample of the AtALMT1 mutant M60A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) / Organ: root / Tissue: root apex / Location in cell: cell membrane |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK-293 / Recombinant plasmid: pEZT-BM |
Molecular weight | Experimental: 120 kDa/nm |
-Macromolecule #1: Aluminum-activated malate transporter 1
Macromolecule | Name: Aluminum-activated malate transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 56.773551 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEKVREIVRE GIRVGNEDPR RIIHAFKVGL ALVLVSSFYY YQPFGPFTDY FGINAMWAVA TVVVVFEFSV GATLGKGLNR GVATLVAGG LGIGAHQLAR LSGATVEPIL LVMLVFVQAA LSTFVRFFPW VKTKFDYGIL IFILTFALIS LSGFRDEEIM D LAESRLST ...String: MEKVREIVRE GIRVGNEDPR RIIHAFKVGL ALVLVSSFYY YQPFGPFTDY FGINAMWAVA TVVVVFEFSV GATLGKGLNR GVATLVAGG LGIGAHQLAR LSGATVEPIL LVMLVFVQAA LSTFVRFFPW VKTKFDYGIL IFILTFALIS LSGFRDEEIM D LAESRLST VVIGGVSCIL ISIFVCPVWA GQDLHSLLAS NFDTLSHFLQ DFGDEYFEAR EKGDYKVVEK RKKNLERYKS VL DSKSDEE ALANYAEWEP PHGQFRFRHP WKQYVAVGAL LRQCAYRIDA LNSYINSDFQ IPVDIKKKLE TPLRRMSSES GNS MKEMSI SLKQMIKSSS SDIHVSNSQA ACKSLSTLLK SGILNDVEPL QMISLMTTVS MLIDIVNLTE KISESVHELA SAAR FKNKM RPTVLYEKSD SGSIGRAMPI DSHEDHHVVT VLHDVDNDRS NNVDDSRGGS SQDSCHHVAI KIVDDNSNHE KHEDG EIHV HTLSNGHLQL EGGSSGGWSH PQFEK |
-Macromolecule #2: ACETIC ACID
Macromolecule | Name: ACETIC ACID / type: ligand / ID: 2 / Number of copies: 4 / Formula: ACY |
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Molecular weight | Theoretical: 60.052 Da |
Chemical component information | ChemComp-ACY: |
-Macromolecule #3: ALUMINUM ION
Macromolecule | Name: ALUMINUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: AL |
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Molecular weight | Theoretical: 26.982 Da |
Chemical component information | ChemComp-AL: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL | |||||||||
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Buffer | pH: 5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 10.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 64.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 3586060 Details: about 1,000 particles were manually picked from the micrographs for 2D classification initially. Class averages representing projections of AtALMT1 in different orientations were selected ...Details: about 1,000 particles were manually picked from the micrographs for 2D classification initially. Class averages representing projections of AtALMT1 in different orientations were selected and used as templates for automated particle picking |
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CTF correction | Software - Name: Gctf Software - details: the CTF parameters of the micrographs were estimated using the GCTF program |
Startup model | Type of model: OTHER Details: the ALMT1M60A/Al/pH5 model was built according to the reference ALMT1apo/pH5 model |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final 3D classification | Number classes: 50 / Avg.num./class: 5 / Software - Name: RELION (ver. 3.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 216946 |